An automated method for operating an automated seed sampling system having a seed loading station, a seed transport subsystem, and a seed sampling station generally includes sensing whether individual seeds are successfully isolated from a bulk of seeds at the seed loading station, and sensing whether the isolated seeds are properly positioned by the seed transport subsystem adjacent the seed sampling station in preparation for removing tissue from the isolated seeds. In some aspects, the method further includes analyzing the tissue removed from the seeds for presence or absence of at least one characteristic, and selecting seeds based on presence or absence of the at least one characteristic.